Contacts of the helix formed by residues 229 - 243 (chain A) in PDB entry 1BK6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASN 3.0 11.9 - - - +
228A LYS* 1.3 85.2 - - + +
230A SER* 1.3 57.1 + - - +
232A ILE* 3.2 8.9 + - + +
233A ARG* 2.7 51.4 + - - +
270A ASP* 5.6 6.9 - - + +
273A THR* 4.8 1.4 + - - -
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.4 18.1 + - - +
228A LYS* 3.0 30.2 - - - +
229A PRO* 1.3 80.0 - - - +
231A LEU* 1.3 74.2 + - - +
233A ARG* 3.0 33.1 + - - +
234A THR* 3.1 12.1 + - - -
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 3.9 24.7 - - + -
190A LYS* 4.2 12.8 - - + -
191A GLU* 3.4 42.4 - - + +
194A ILE* 4.1 13.5 - - + -
223A LEU* 4.5 30.7 - - + +
226A SER* 4.0 20.6 - - - +
228A LYS* 3.4 13.8 + - + +
229A PRO 3.4 0.8 - - - -
230A SER* 1.3 81.2 + - - +
232A ILE* 1.3 58.0 + - - +
234A THR* 3.3 1.7 + - - -
235A ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU 4.2 8.1 - - - +
224A PHE* 4.1 27.3 - - + +
226A SER* 3.2 38.6 - - - +
227A ASN 4.4 3.8 - - - +
228A LYS 3.2 16.7 + - - +
229A PRO* 3.2 11.5 + - + +
231A LEU* 1.3 77.4 - - - +
233A ARG* 1.3 55.8 + - - +
235A ALA* 4.0 6.7 - - - +
236A THR* 2.5 42.4 + - - +
265A LEU* 4.4 10.8 - - + -
273A THR* 4.7 7.9 - - + +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PRO* 2.7 30.9 + - - +
230A SER* 3.0 30.4 + - - +
232A ILE* 1.3 76.7 - - - +
234A THR* 1.3 63.9 + - - +
236A THR* 3.4 3.7 + - - -
237A TRP* 3.2 21.5 + - - +
270A ASP* 3.0 31.7 + - - +
272A GLU* 3.7 39.4 + - + +
273A THR* 3.6 21.0 - - - +
276A ASP* 5.1 2.3 - - - +
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 2.9 27.3 + - - +
194A ILE* 3.5 22.0 - - + -
195A TRP* 3.8 35.4 - - + -
230A SER 3.1 6.7 + - - -
231A LEU 3.3 2.4 + - - -
233A ARG* 1.3 73.7 - - - +
235A ALA* 1.3 62.2 + - - +
237A TRP* 3.3 17.1 + - + +
238A THR* 3.0 32.2 + - - -
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 3.8 13.2 - - + +
220A ILE* 4.9 3.6 - - + +
223A LEU* 4.0 26.5 - - + -
224A PHE* 3.5 27.9 - - + -
231A LEU 3.0 17.1 + - - +
232A ILE* 4.0 4.3 - - - +
234A THR* 1.3 77.2 - - - +
236A THR* 1.3 57.3 + - - +
238A THR* 3.9 1.4 - - - -
239A LEU* 3.0 28.2 + - - +
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.5 15.6 - - - -
232A ILE* 2.5 25.1 + - - +
233A ARG 3.6 5.6 - - - -
234A THR 3.2 0.2 - - - -
235A ALA* 1.3 75.6 - - - +
237A TRP* 1.3 65.0 + - - +
239A LEU* 3.3 8.4 + - + +
240A SER* 3.1 20.1 + - - -
265A LEU* 4.1 7.6 - - + +
273A THR* 3.5 41.4 - - + +
276A ASP* 3.9 5.7 - - + +
277A ALA* 3.7 21.8 - - + +
280A ALA* 5.5 1.0 - - - +
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Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TRP* 3.9 23.8 - + - -
198A GLY* 3.8 22.4 - - - -
199A ASN* 3.7 20.4 - - - -
233A ARG 3.2 10.2 + - - +
234A THR* 3.6 16.2 - - + +
236A THR* 1.3 80.5 - - - +
238A THR* 1.3 70.8 + - - +
240A SER* 2.8 28.5 + - - -
241A ASN* 3.2 24.8 + - - +
276A ASP* 3.7 30.4 + - - +
127C LYS* 3.5 36.3 - - + +
128C LYS* 4.2 0.4 - - - -
129C LYS* 3.5 53.4 - - + +
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 2.8 42.2 + - + +
197A LEU* 4.2 7.0 - - + +
198A GLY* 3.4 30.5 - - - +
201A ALA* 5.3 1.1 - - + -
220A ILE* 4.9 2.2 - - + -
234A THR 3.0 17.7 + - - -
235A ALA 3.9 4.3 - - - -
237A TRP* 1.3 82.2 - - - +
239A LEU* 1.3 63.3 + - - +
241A ASN* 3.1 14.5 + - - +
242A LEU* 3.2 27.3 + - + +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A MET* 4.1 24.7 - - + -
220A ILE* 4.6 12.5 - - + +
221A LEU* 5.3 1.8 - - + -
224A PHE* 4.3 19.3 - - + -
235A ALA 3.0 18.5 + - - +
236A THR* 3.4 7.9 - - + +
237A TRP 3.2 0.2 - - - -
238A THR* 1.3 76.4 - - - +
240A SER* 1.3 63.0 + - - +
242A LEU* 3.3 12.8 + - + +
243A CYS* 3.1 30.4 + - - -
258A ALA* 4.1 19.3 - - + -
261A THR* 5.5 1.8 - - + -
262A LEU* 3.3 34.3 - - + -
265A LEU* 4.8 5.4 - - + -
280A ALA* 5.0 4.9 - - + -
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A THR 3.1 11.1 + - - -
237A TRP* 2.8 20.0 + - - -
239A LEU* 1.3 76.9 - - - +
241A ASN* 1.3 62.9 + - - -
243A CYS* 3.2 2.3 + - - -
244A ARG* 3.0 23.9 + - - +
276A ASP* 3.7 26.9 + - - -
279A TRP* 4.0 7.4 - - - +
280A ALA* 4.1 12.3 + - - +
283A TYR* 3.7 20.0 + - - -
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Residues in contact with ASN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLY* 3.2 24.3 + - - +
201A ALA* 4.0 23.5 - - + +
202A GLY* 4.0 7.7 - - - -
208A ARG* 3.8 7.1 - - - +
237A TRP* 3.2 30.0 + - - +
238A THR 3.1 7.8 + - - +
240A SER* 1.3 79.4 - - - +
242A LEU* 1.3 61.8 + - - +
244A ARG* 3.3 30.0 + - - +
127C LYS* 3.4 32.4 + - - +
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA* 3.7 24.0 - - + -
208A ARG* 3.3 28.0 - - + +
211A VAL* 4.1 13.7 - - + -
212A LEU* 3.8 35.8 - - + +
216A ALA* 5.9 0.2 - - + -
217A MET* 4.4 15.0 - - + -
220A ILE* 3.8 28.3 - - + -
238A THR* 3.2 20.6 + - + +
239A LEU* 3.5 14.8 - - + +
240A SER 3.2 0.2 - - - -
241A ASN* 1.3 76.6 - - - +
243A CYS* 1.3 60.6 + - - +
250A PRO* 3.6 11.3 - - - +
255A VAL* 3.9 4.4 - - + +
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Residues in contact with CYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A MET* 5.8 0.7 - - - -
239A LEU* 3.1 31.4 + - - +
240A SER 3.2 4.0 + - - +
242A LEU* 1.3 77.4 - - - +
244A ARG* 1.3 64.3 + - - +
245A GLY 3.6 2.8 + - - +
249A GLN* 5.4 0.2 - - - +
250A PRO* 3.6 15.6 - - - +
255A VAL* 4.2 18.4 - - - -
258A ALA* 5.4 2.9 - - - -
262A LEU* 5.4 0.9 - - - -
280A ALA* 4.1 14.6 - - - +
283A TYR* 3.6 25.2 - - + +
284A LEU* 3.8 34.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il